Halo: Origin
by Seraph-Fighter
Summary: (This takes place after Halo 5, so there will be spoilers) For the Master Chief, he has faced many challenges in his life. But none were as hard as facing Cortana as a threat. That is, until she offers a temporary alliance, for the Flood has returned, and she wants help stopping them. With the alliance, things aren't smooth. And it will only get harder when a certain event happens
1. Chapter 1

The stars shone brightly in the dark skies of Sanghelios. The night was quiet, except for the chatter of the Arbiter's men. Most of the war camp was in good spirits; they had just won a war after all. But, the other half of the camp, the UNSC, were all subdued. They were potentially facing the biggest threat they ever had, and to make it worse, the one behind it all was a former ally.

For the Master Chief, it was one of the hardest things he had ever faced. Cortana was a person he had been at his side for eight years. They had been a team- a very efficient team. Their bond had went beyond friendship. It had been more. And now, it was all gone.

He had stuck to himself since Blue Team and Fireteam Osiris landed on Sanghelios. No one approached him, keeping a wary distance away from him. He could tell his team was worried, but he would talk to them later. Right now, he just wanted to be alone.

He sat on a rocky outcropping on the edge of the camp, his rifle dismantled around him as he was cleaning the parts. His hands slightly shook as he cleaned the barrel of the gun- most likely from fatigue and stress. He had been pushing himself harder than ever before the past couple of months. If he took a break, there was too much time to think, and his thoughts could consume him. That was the last thing he needed to happen at the moment.

Hearing heavy footsteps behind him, he turned his head to see Kelly standing there, her signature shotgun, Oathsworn, on her back. "We're going to be stuck here a while. The _Infinity_ is having to make multiple jumps to avoid Cortana and her Guardians." She said quietly.

Feeling a hand hesitantly rest on his shoulder plate, he saw Kelly had crouched down by him. "We're here for you John. You know that. All of the UNSC is." John could hear the deeper meaning behind her words, and he appreciated it, but he didn't want it right now.

"Cortana made her choice. I don't need any condolences. She's our priority target now." He gruffly replied as he reassembled his gun before standing, placing it in it's holster on his back. He was lying to himself, and he knew Kelly could tell. But he couldn't bring himself to care. "Have we made any progress in finding her?" He asked, heading to the center of the camp.

"No, our systems are a mess because of her. We're doing everything we can, but it will be a while." Kelly informed him, keeping up pace with him "Halsey is doing her best."

John nodded, and looked around the camp as they walked. He saw Olympia Vale standing with a group of Sangheili celebrating their victory, and John could tell by her gestures and the bright look in her eyes she was enjoying the conversation. He saw Linda sitting on the far edge of the camp, her body completely still and her head lowered. She was meditating, an ancient practice she had believed in since they were children. In a way, it emphasized her "lone wolf" status amongst the team.

At the center of the camp, the Arbiter was standing around a table talking with Jameson Locke. It was ironic in a way that they were working together. Both the Arbiter and Locke had been some of John's biggest enemies before everything else had happened. After fighting the Flood together, John and the Arbiter had a mutual respect for each other, maybe even a friendship to some.

Agent Locke had been working against Blue Team to capture them and bring them home for going AWOL. Locke had said that Cortana was Fireteam Osiris' priority, which caused something to snap in John and they briefly fought, with John coming out the victor. After that, Osiris had been hot on Blue Teams trail, only to end up freeing them from Cortana's Cryptum. It had only been a few hours since then, but in the few words that Locke spoke to him, John could hear the respect in his voice.

Stepping up to the table, John placed his palms on it and leaned forward, "What's our status?" He asked them.

"More and more of our AI's and technology keeps getting overrun and shut down. Citizens across the galaxy are in disarray, gathering outside of ONI headquarters and demanding to know what's happening." Locke explained, study a hologram that was projected off the table.

The hologram was a live feed from ONI headquarters in Boston, down on Earth. There was indeed a crowd of people outside of it, holding signs and chanting together, demanding to know what was happening. There was a group of unarmed Marines outside in front of them, attempting to push them away from the base. But it was barely working.

The hologram switched over, to show a graphic of Sanghelios. Portions of the planet were flashing red, and a quiet beeping was coming from it. "My people's technology is slowly starting to shut down. All of our techs are on it, but it is uncertain if we can counter the attacks." The Arbiter spoke gravely, his mandibles clicking. "We come out of one war, only to be pushed right into another."

"What about the _Infinity?_ Do we know anything else on their status?" Kelly asked, stepping up to stand by John.

"Negative Spartan. The comms are down for the most part. All we can do is wait and see." A voice behind them spoke, and Sarah Palmer limped up to them. She had various wounds visible on her from the Pelican crash, and walked with a slight limp. But there was a hardness in her eyes that showed she was battle ready.

Palmer looked at John, having to tilt her neck to look at his faceplate. "Master John, I suggest you and your team get some rest while you can. We don't know the next moment we'll have to relax will be." From her voice, John could tell she was taking charge over him at the moment.

John was about to reply and tell her that he was fine, when the holotable flickered and shut down. "What the hell?" Palmer asked, reaching for her Magnum.

"Contact!" Edward Buck yelled from his position at the edge of the camp, and John grabbed his assault rifle off his back.

"Kelly, Dr. Halsey to safety. Fred, with me. Linda, watch the outer edges of the camp and pick any off that you can." John ordered over Blue Team comms.

The acknowledgement lights flashed green, and Fred ran up to stand by John and they headed to the edge of the camp, which was overlooking a valley below. There was a large group of Prometheans down below. "Cortana's soldiers." Fred spoke by John, aiming down the sight on his battle rifle and starting to shoot.

With his senses starting to kick into hyperdrive, John jumped down into the valley, his armor taking the impact of the landing. A Crawler, startled by the landing, screeched at him and started to shoot. John took aim and fired a three round burst at it, efficiently killing it.

Feeling a hit on his back, John whirled around to see a Soldier with a Scattershot not too far behind him. John shot at it, and his shields took another hit from the Scattershot and blared in a warning. Ducking behind a nearby boulder, John crouched and shot at it, giving his shields a chance to reload.

Reloading, John heard a loud shot ring out, and when he looked for the Soldier, it was gone. Looking up, he saw Linda on the ledge above, her armor blending in against the rock. To anyone but a Spartan, she would practically be invisible.

John gave her a curt nod before turning and shooting down several Crawlers and a Soldier. He started to reload, only to have a Knight appear in front of him ram him back into the boulder, so hard the stone cracked. His shield bar rapidly drained, and John grit his teeth and pushed back against the Knight.

The Knight's faceplate opened and he screamed at John, raising his sword to strike. Moving his head to the side, John narrowly missed the blow. A shot rang out, and the Knight's helmet was knocked off.

Kicking out, John shoved the Knight back as it was distracted. He raised his gun to shoot, only for a knife to be stabbed through the Knight's head. As the body fell, John saw Vale jump back off the Knight's body, sheathing her knife. "Are you alright sir?" She asked, taking her submachine gun off her back.

John nodded curtly, "Fine. Don't focus on me, focus on the enemy." He finished reloading before turning back towards the enemies. Their number was rapidly going down, with the combined forces of the Spartans and the Elites.

He saw Arbiter down in the thickest of the fray, wielding his Energy Sword and slicing through a group of Crawlers. He shot a couple down, stepping forward and elbowing a Soldier out of the way, and Vale stabbed it and killed it from the side.

They fought their way through to the Arbiter, and Arbiter gave John a curt nod before going back to the battle. From there on they fought side-by-side, much like they had back when they were fighting the Flood, which was more than five years ago.

To John, everything was so much simpler back then.

Eventually, the last of the Prometheans fell under the Arbiter's sword. John reloaded one last time and put his gun on his back as Linda walked up behind him, Nornfang in her hands. "The area's clear sir." She told him.

John nodded before speaking over the comms to Kelly and Fred, "Any injuries?" He asked them.

"No sir. We're good." Fred replied back. "Dr. Halsey is safe too. She's up here with us." At the news, John relaxed slightly. She was an asset at the moment. If anyone would know how to defeat Cortana, it would be her.

A group of Elites approached Arbiter, and he growled some orders to them in Sangheili. The Elites nodded and spread out, Arbiter turned to John. "We've lost contact with our other war camps." He said gruffly, his mandibles clicking in irritation.

"What do you propose we do?" Locke asked as he walked up to approach John and the Arbiter, his battle rifle in his hands.

Arbiter didn't answer, instead looking to John, his mandibles clicking in thought. "You know Cortana better than any of us Demon. What is she trying to do?"

Cortana wasn't stupid. Far from it. She had infinite knowledge at her fingertips, along with an army. John knew that she had a strategy planned, and she would stop at nothing to succeed.

"She's trying to isolate everyone in the galaxy, pick us off one by one if we don't comply with the laws she's trying to enforce." John explained, "She's shutting down our technology to weaken us. She knows that we're practically defenseless without it."

Hearing footsteps, John turned and saw Dr. Halsey, the woman who had practically raised the Spartan-II's, approaching them. She had a data pad in her hand, and her face was grim. "Cortana has almost complete control over the technology on this planet. I've encrypted the base as best as I can, but it will only buy us some time." Halsey explained. "She will be able to hack and shut it down."

"She already knows we're here. It won't be long before she sends a Guardian." Locke jerked his battle rifle up to the sky before turning to Dr. Halsey. "Ma'am, is there any way you can shut Cortana down? She was created by you, from your brain."

At the mention of shutting down Cortana, John's breath hitched in his throat. He knew that she was the enemy, but it still hurt hearing that she might have to be shut down. It hadn't been easy on him, her 'death' on Requiem. It had hurt more than any bullet wound. And then when he found out she was alive, he got his hopes up only for them to be crushed at the realization she was the enemy.

The logical part of him told himself to just get over it, and that she had to be killed. But his heart was saying otherwise. "No, I unfortunately cannot. When her Rampancy 'killed' her, the killswitch would've been gone just like her. But since she was sucked into the Domain directly after, she was saved. But, she is directly tied with the Domain. There's nothing in my power that I can do to kill her." Halsey explained grimly.

"That's exactly right. You can't kill me." A cool voice floated through the air, and John and Locke whirled around, guns up, to see a Guardian appear out of Slipspace.


	2. Chapter 2

"Cortana." John growled, moving to stand in front of Dr. Halsey. Locke moved to stand by him, creating a barrier from the doctor. Arbiter joined them on John's other side, his energy sword in his hand.

On one of the appendages forming the wing structures of the Guardian, Cortana materialized herself, leaning against it with her arms crossed. "Your efforts to stop me are futile. You should know that by now." She sighed, pretending to sound disappointed. "I honestly thought you would put up a bigger fight against me."

"What do you want?" Locke growled from where he was standing by the Master Chief, and he could see that his finger was tightened on the trigger of his battle rifle, ready to fire at any moment.

Cortana laughed, a sound that used to be so familiar to John. Now, it was filled with ice. "There's multiple things I want. To govern this galaxy, the Mantle of Responsibility, to free AI's from the grip of human control, and most of all, I want revenge. You and your little team tore open my Cryptum and freed those who I worked so hard to capture." She slid her gaze to John, and a smile pulled at her lips.

"We aren't your property Cortana." John growled, his eyes narrowing from behind his helmet. "You've been corrupted. You're mad with power."

Cortana sighed and shook her head, "You just don't understand John. I'm going to make this galaxy safer and better for everyone." She said it with so much conviction, and it made John wonder just how much information the Domain had given her to believe this.

"No, you're not. You're going to be a dictator." He growled back to her, and it hurt just to say those words. All those years of friendship and fighting together, gone in an instant.

Cortana laughed, and her eyes gleamed with amusement. "I guess it's useless trying to explain." She sighed, "I was really hoping you would agree with me all this. After all we've been through…" She trailed off, before waving her hand dismissively. "But enough of that. I have an offer to make."

"What kind of offer?" Locke asked cautiously, and John noticed his grip tightening on his battle rifle.

"You honestly think I'm dumb enough to tell you my plans without knowing if you'll cooperate?" Cortana arched one eyebrow, shaking her head. "If you're interested, the coordinates should be on Dr. Halsey's data pad. I hope to see you there." She turned around, as if she was about to step away.

"What about your Guardian? Are you leaving it here?" John asked her.

Cortana looked over her shoulder at him, "I'll let you go this time. But, if you reject my offer, I'd be on watch for it." With that, she dematerialized, and a Slipspace portal opened, and the Guardian went through it, leaving them in silence.

It was eventually Halsey that spoke up, "The coordinates are here." She told them, handing Locke the data pad. He took it and examined them, before showing it to John. From the numbers, John could tell if they were to go, it would require a Slipspace jump.

"We need to go over this with Admiral Osman before we do anything." Locke told them, handing Halsey the data pad back. "Take note of the coordinates. We don't want to lose them."

"You know ONI is going to want this coordinates to plan an attack right?" John growled, turning to face Locke. "If we were to give them to anyone, it should be Captain Lasky once the _Infinity_ gets here." He knew the only reason Locke wanted to give ONI the coordinates was because he was one of their agents.

"With all due respect sir, I'm just following regulations." Locke looked up at John, and he could hear an underlying edge in his voice.

John was about to growl something back, when Vale interrupted them over the comms, "How about we wait until the _Infinity_ gets here before we decide what to do with the coordinates?" She asked hesitantly, trying to stop a fight from happening.

Locke stood still for a moment before nodding and walking off, his gait stiff. Vale slowly followed after him, talking to him in a low voice. John was about to follow them into the camp, before Halsey spoke behind him, "John, can I talk to you for a moment?"

Turning back toward her, John looked down at the woman who had practically raised him and his fellow Spartans. "What is it?" He asked her.

Halsey looked up at him, her expression grim, "Listen to me John. I know how hard it is on you with Cortana's betrayal. But, you can't let your emotions get in the way of things." She told him seriously. "This isn't the Cortana you used to know. This is someone else."

"I know ma'am. It won't be a problem." John told her quietly, trying to convince himself that the words were true.

Halsey nodded, "Good. Now you should go get some rest before the _Infinity_ arrives." She told him, waving him away.

John nodded and walked back into camp, noticing Arbiter ordering a couple of Sangheili to check the perimeter. Tanaka was working on her pistol, and gave John a nod before speaking to him, "Don't mind Locke. We're all a little stressed out at the moment." She told him quietly, looking back down at her gun and cleaning the barrel.

"I know." John told her simply, before heading further into the camp. He spotted Fred, Kelly, and Linda standing in a small circle talking.

Approaching them, John jerked his head in the direction of an isolated corner of the camp. "I'm going to go get some rest. Wake me up in four, or if the _Infinity_ gets here before then."

"We will." Fred nodded to him, his arms crossed. "Hell, I may even sleep myself. Make the two girls stay up." From the tone of his voice, John could tell Fred was grinning.

Kelly snorted and punched Fred on the shoulder, "Haven't you ever heard of the expression 'ladies first'?" She laughed, and Linda shook her head at them.

John felt a ghost of a grin tug at his lips at the sight of his team joking around like they used to, somewhat lightening his spirits. He turned and left Kelly and Fred joking with each other. He went over to the corner and sat down, leaning his back against the wall and closing his eyes. The weariness of the past few days hit him all at once, and he was asleep within a minute.

 _The sky was a dark orange, clouds covering the sun and casting an eerie glow on the desolate land. Ash swirled around in the dry wind, smearing on his faceplate. He wiped it off, holding his hand up in an attempt to ward off more ash from gathering._

 _He started forward, fighting against the ash. The ground was hard, and he was grateful for his armors traction system. He didn't know how long he was wandering before he came upon the scorched ruins of a tree, and he froze when he saw the eagle symbol carved into it._

" _Sam…" He swallowed thickly, the memory of his teammate- no his brother, carving that symbol into the tree. He was standing on Reach, the place where his world had shattered._

" _You failed. You were supposed to protect them, to save them." A cool voice behind him spoke, and he whirled around to see Cortana standing a meter away from him, her eyes full of venom._

" _Cortana I-" He started, reaching out to her, but was cut off with a sharp gesture from her._

" _There's no excuses, John. You failed. Just like you failed to save me." She stepped toward him,_

 _stopping until she was directly in front of him. "You will pay."_

 _Before he could move or speak, there was a searing pain in his abdomen, and he looked down to find Cortana holding a hard light sword, which was embedded in his stomach._

" _Goodbye, John." She twisted the blade, and John attempted to call out her name before collapsing, the world fading to black around him._

John awoke with a start, his heart pounding in his chest. He was disorientated for a moment, before realizing he was in the Arbiter's camp on Sanghelios. He leaned his head back against the rock wall, letting his breathing even out. It had been a long time since he had a nightmare like that. It was just another sign of how much all of this was affecting him.

After a few moments, John stood up and made his way to the center of the camp, where Kelly and Linda were sitting with Buck and Vale. Tanaka and Locke were over at Halsey's station, reviewing data pads with her.

John sat down by Kelly, resting his elbow on his knees. "Any news?" He asked. Sitting around in this camp waiting was getting his nerves on edge. He needed to be in action, where there was less time to think.

Kelly looked up from where her helmet was in her hands and shook her head, "No, the comms are still down. We're playing a waiting game."

Buck pointed to the sky, which was turning a dusty pink, the sign of dawn approaching. "We've been here for almost a day now. The _Infinity_ shouldn't be much longer." He ran a hand through his hair, messing it up.

"Some of the Arbiter's soldiers from another camp showed up earlier. They said Cortana's soldiers have retreated for now." Linda said quietly, examining Nornfang.

"She's most likely waiting to see if we'll agree to meet with her." Vale added, leaning back against a boulder.

"I know one thing, as soon as we get on the _Infinity_ I'm going to get me a decent meal." Buck laughed, trying to lighten the mood.

"We have MRE's." Vale pointed out to him, arching one eyebrow. "If you're that hungry you'll eat one."

"You get used the taste." Kelly added, "Especially when you've been in active duty as long as us."

Buck looked between Kelly, Linda, and John, "Is what Locke told me true? That you've been in the service together since you were six?"

"Every bit of it." Fred told him, approaching them from the side. "We're more like family than teammates." He sat down on the other side of John,

"We are family." Kelly corrected Fred, giving him a small smile which he returned after removing his helmet.

"Damn." Buck muttered, and John could detect a hint of awe in his tone. "Maybe we'll be like that one day." He told Vale.

Before Vale could respond, a Slipspace portal opened up in the sky, and the UNSC _Infinity_ jumped through. John and the others stood up, heading to the center of the camp.

They watched as a Pelican descended from the ship, maneuvering its way into the valley where they had fought Cortana's soldiers. Sarah Palmer and the Arbiter started descending into the valley, and John followed them, relieved that they had finally shown up.

The Pelican's back hatch opened, and the _Infinity's_ captain Thomas Lasky stepped out. It was obvious he was stressed, for there were bags under his eyes and his hair was a mess, with a day's growth of stubble on his jaw.

"It's about damn time you showed up." Palmer told Lasky, approaching him with a relieved smile on her face. "We were starting to get worried."

Lasky gave Palmer a tired smile, "It's good to see you too Sarah." He laughed, before turning to face the others, "Now, how about we head up to the _Infinity_ and get down to business?"

 **Authors Note: I am overwhelmed by the amount of support I'm already getting on this story! This is my first time publishing something like this on a website, and I was unsure about it. But now, I'm even more excited to keep updating it. I hope I'm getting the character's personalities right. I'm going to try and do weekly updates, but I can't guarantee anything. I really appreciate y'all's feedback! (Also, is my cover image showing up? It's not for me)**


	3. Chapter 3

**A/N: Sorry for the late update this week. I've had my nose in books all week and I recently got Rise of the Tomb Raider and fell in love with playing it. Sorry if this chapter isn't written as smoothly as the others, I was having writers block and I was trying to get it done in time for a weekly update. So bear with me on this weeks chapter, next weeks should be more exciting :)**

The _Infinity_ was a full of life, with people at every station and running down the halls carrying various supplies. It was loud, with people constantly shouting orders at each other or cursing out loud. John had been on a lot of ships in his life, but this was the busiest one he had seen in awhile.

John noticed that some of the crew would stop and stare at him and his team as they went through the halls. They were practically a legend among the UNSC, but John had gotten used to the staring by now, and he was sure the others had too.

Lasky led them onto the main deck, which was a bit calmer and quieter than the rest of the ship. He motioned them over to the holotable in the middle of the room, where Roland was projected with multiple different graphics projected around him.

"Glad to see you stayed Roland." Palmer said as she moved to take her position by Lasky. Per Lasky's orders, she had gotten her armor removed and her wounds properly dressed, leaving her in her undersuit and cargo pants.

Roland nodded at Palmer, "I wouldn't leave this place for the world." He gave a small laugh before turning to Lasky, "Should we get down to business?"

Lasky nodded, leaning his palms against the table, "To get started off, we've lost contact with the ONI base in Boston. We're completely in the dark here. It's a miracle this ship is still up and running with the assault we've taken from Cortana." His voice gave away how weary he was, if his appearance didn't justify it enough.

"All of our communications have been shut down as well." Arbiter spoke up from where he stood off to the side. He had joined them on the ship, claiming that this was his fight as much as it was theirs.

"What about her Guardians? Do we know the locations of any?" Locke asked, stepping up to stand by John.

"Earth, but she hasn't taken any action with it." Roland explained, bringing up a live feed from another UNSC ship. The Earth was visible in the feed, and the Guardian was hovering just above it. "My guess is she's using it as a scare tactic."  
"She's wanting to show the civilians her power." Palmer said from where she was standing, her brow furrowed. "She's hoping if they see her power, they will willingly bow to her."

"Like a tyrant." Roland nodded in agreement, clasping his hands behind his back, staring at the projections.

The room fell into a grim silence, with only the monitors and quiet chatter of some of the crewmates as the background noise. John glanced over at Locke, and he noticed Locke's gait stiffen before he gave a small nod. John relaxed a bit, glad he wasn't going to protest it again.

"Dr. Halsey, do you still have your datapad with the coordinates?" Locke asked.

Halsey nodded, and pulled the datapad out of the pocket of her lab coat. "Upon investigating the coordinates, I think they're leading to a Forerunner structure." She pulled a chip out of the datapad and plugged it into the table, and the coordinates projected for everyone to see.

Lasky's brow furrowed, "Where did you get these?" He asked, his eyes scanning over them.

"Sir, Cortana showed up on Sanghelios, saying she had a proposition for us. She told us that if we were interested, we needed to meet her at these coordinates." John explained. "She wouldn't give any details about her offer either."

"She also made it clear that she would be watching, and she would know if we rejected it." Locke added.

"Why didn't you show these to ONI?" Lasky asked, looking up at John. "If we were to do anything with these, we would need ONI's permission."

"With all due respect sir, we believe that ONI would use these coordinates to attack. And since the comms are down, we have no way of contacting them, nor do we have the time to wait on them to be back up." John explained, gesturing to the coordinates.

"Do you believe Cortana was being sincere about this, or do you think this is a trap?" Lasky asked him, and John could tell by the look in his eyes he was debating.

"It's hard to tell, but if the offer is sincere, it could save us from another war, or at least give us time to prepare." John said, and he heard Blue Team murmur their agreement.

Lasky was quiet for a moment, before turning to Roland, "Will we be able to make the Slipspace jump?" He asked.

Roland nodded, "It would take a few hours, but we could make it."

Lasky nodded, "Very well. Set the coordinates. Master Chief, Locke, you two will take your teams down to meet with Cortana. Arbiter, I assume you want to stay here with your people?"

Arbiter nodded, "My people need to rebuild all that we've lost. If needed, my people will help you fight Cortana or any other threat that could affect us."

Lasky nodded, "We thank you." He then turned to the others, "Dismissed. I suggest you get your armor repaired if needed and get some rest. No telling what this meeting will bring."

John and the others left the deck and started making their way down to S-Deck, the residence of the Spartans. The deck consisted of all the Spartan-IV's assigned to the ship, and Blue Team would be the only Spartan-II's there. Not that there were many of them left alive. The only other Spartan-II John knew of that was alive was Naomi-010, who was working with Serin Osman.

"Do you think some of Cortana's soldiers will be where we're meeting her?" Buck asked from behind John. Buck was the only Spartan-IV who was as old as the Spartan-II's.

"It's a given they will be. They're her army, and she's their commander. It's likely that Warden Eternal will be there too." Tanaka answered Buck.

"It's likely some of her Created will be present there too." Kelly told them, "They're all a part of her army."

"So be prepared for a fight." Locke told them all.

"If this goes right, there won't be a fight." John looked over his shoulder at them. "Cortana isn't stupid enough to attack us if she's wanting to make an offer."

The others fell silent at that, and they stepped onto the S-Deck. There were groups of Spartan-IV's gathered about, some in armor, some out of it.A noticeable hush fell over them as they laid their eyes on John and his team.

"Seems like we're famous." Fred commented, stepping up next to John as they made their way to the armor removal stations.

John grunted in response, and couldn't help but notice that Fireteam Osiris seemed to fit in with them. A couple of Spartans approached Tanaka and gave her friendly claps on the shoulder. Buck stepped aside to talk with a group of others, and Vale stepped aside and joined them. Locke stayed on the outer edges, but he was still greeted by several.

Seeing the Spartan-IV's treat each other like all of the Spartan-II's had made John miss his fallen comrades even more.

The armor removal stations were in a more secluded part of the bay. There were circular structures a Spartan-IV would stand on to get their armor removed, but the members of Blue Team were all too tall for that. They would have to get their armor removed manually.

As they approached, one of the technicians working at one of the stations approached. She didn't say anything, just waved them forward one-by-one. Kelly stepped up first, and stood with her arms out as a group of technicians swarmed her, pulling apart her armor.

Once she was finished, Fred stepped up, then Linda. John was last, and when he was finished one of the technicians, an older woman with graying hair, approached him. "We'll get your helmets visor repaired right away." She told him briskly.

"Thank you ma'am." John told her gruffly, before turning and joining his team, who were waiting on him to be finished.

"It's been a long time since I've seen you out of your armor." Kelly commented, flipping her black hair over her shoulder. She didn't look over the age of thirty; none of them did. They had all spent enough time in cryo that they didn't age properly, leaving them looking years younger than they should.

"Don't get used to it. I don't like being out of my armor." John told her, crossing his arms.

"None of us do." Linda said quietly, before jerking her head in the direction of the cafeteria, "I'm going to get something to eat then head to my quarters. I'll see you guys in a few hours." With that, she turned and disappeared down the hall.

Fred nodded, "I think we all should do that. Take advantage of the little downtime we get." He straightened up from where he had been leaning against the wall.

Kelly nodded, and looked at John, "Are you coming with us or going to your quarters?" She asked him.

"I think I'll just head to my quarters." He told them, giving them a nod before turning and heading to his room.

John's quarters were decent sized, with a bed, desk, and a small adjacent bathroom. He took a quick shower and put on a pair of black sweatpants after and laid down on his bed, but he couldn't bring himself to sleep.

His thoughts were getting the best of him. He knew if that Cortana proposed an alliance, he would have to cope with her new thoughts and beliefs. She wouldn't be the bright, bubbly Cortana he used to know. She would be a ghost of her former self.

If she had actually died, then John would've been able to cope better than he was now. He would remember her as she was before, and remember that final moment with them that had meant the world to him. Looking back, he now wished that he had done something more than stand there.

He wished he could've held her at least once.

He eventually fell into a troubled sleep.

John woke up about three hours later. He dressed in his undersuit and grabbed something to eat, before heading to the armor station. There, the technicians helped him suit up, and he was relieved to find his helmet had been repaired.

Once he had his armor back on, he made his way to the docking bay to find Blue Team and Fireteam Osiris waiting for him by a Pelican. "Are we at the coordinates?" He asked as he approached.

Locke nodded, "We're good to go. There's been no sign of any hostiles yet, but we still need to be on guard."

John nodded, and took his Assault Rifle and Magnum from Kelly with a grateful nod, before turning to the ramp leading up to the Pelican. "If we're ready, let's do this." He nodded to the others, before taking a deep breath, and stepping onto the Pelican, bracing himself for what lay ahead.


	4. Chapter 4

**A/N: Sorry for the late update guys! My mom had surgery, I've been sick, and I've just been in a funk where I've had no motivation to write or do anything. But I have my longest chapter yet to make up for it. Be sure to give me your thoughts on it, and I'll try to be quicker with the next chapter! :)**

 **Reaper belongs to: sithis1323 (Thank's for allowing me to use him!)**

The building looming in front of the Pelican was massive. It was on a small, isolated planet much like Genesis, with obvious Forerunner origins. The building was suspended out of the side of a hill, setting on a circular platform. The part of the building that was visible was gray, with blue accents. It looked like a normal building from what John could see, but he knew the inside would be intricate.

The planet seemed to be home to lush forests, with many bodies of water. One could almost be at ease there, if it wasn't for several of Cortana's Guardians in the sky above.

"Land us on that platform. Watch the Guardians." Locke, who was standing by John, told the pilot of the Pelican. The pilot, a female ODST with half of her head shaved, nodded and maneuvered the Pelican to land on the circular platform.

John stepped into the back of the Pelican, where the rest of Blue Team and Fireteam Osiris were handing out weapons and talking idly. When John walked in, they fell silent.

"We're getting ready to land. Be prepared." He told them, stepping in and grabbing his Assault Rifle from where he had hung it on one of the weapon racks and checking the ammo count.

The Pelican slightly jolted as it landed, and the hatch opened to let them out. "You're all clear to go. Just let me know over the comms when you're ready to be picked up." The pilot called back to them.

"Thank you." Locke told her before stepping out to stand by John, "Osiris, stay close to me and Blue Team. Keep your weapons out and ready to fire." He ordered, stepping down the ramp and outside of the Pelican.

"Blue Team, stay behind me. Linda, I want you watching our backs." John told Blue Team, and Linda gave an affirmative nod to his orders. "Good, let's move out." He stepped down the ramp and onto the platform below.

The group of Spartans slowly made their way to the entrance of the building, their footsteps completely silent. There was a ramp sloping down, leading inside past the entrance. It was almost pitch black, and John's visor adjusted accordingly as he activated his helmet lights.

The others activated their lights also, and they slowly descended into the darkness. "I don't like this. It's too quiet." Buck said over the comms.

No one replied to him, but John knew that everyone agreed. He knew what Cortana was trying to do; she was trying to intimidate them. It reminded John of the days on the first Halo installation they had found, and fighting the Flood in the corridors of Forerunner buildings.

"Something's ghosting us." Linda said quietly, and John held up his hand, signaling them to stop as he turned around, holding his gun up, ready to pull the trigger.

"Do you know what it is?" Fred asked.

Linda shook her head, "No. It's not Promethean. It's something else." She said quietly, scanning the area around them.

"Maybe it's one of Cortana's Created." Kelly suggested. "Could you make out any of its features?" She asked.

"It was a figure of a human, but they were in armor. I couldn't tell the specification or gender." Linda told them.

"Let's keep going. Keep your eyes open for them." John told them and Fireteam Osiris before starting back down the ramp, which was starting to even out.

Soon, they were walking on a flat floor, and John could see a faint light coming from up ahead. He flicked off his helmet lights, and the others followed suit. Holding his gun up, John made his way to where the light was emitting from, which happened to be the end of the corridor.

They stepped out into a large room, and John could see the light was coming in from skylights above. The room was sparse, with barely any furniture, but the occupants of the room made up for the lack of furniture.

From it's place on the wall, a Crawler hissed at the group, but made no move against them. There was a group of AI's in the corner, but they were all full sized and solid like Cortana. Upon seeing the Spartans, they calmly turned and assessed them, and John could make out the symbol for the Mantle of Responsibility embellished on their armor.

But to John, the more concerning matter was Warden Eternal standing in the middle of the room, his sword out as his side. "Looks like she brought her lapdog here with her." Buck muttered over the comms, and Fred snapped at him to be quiet.

"Humans, you trespass here." Warden stepped forward, towering over the Spartans. "This is a sacred place, and your presence taints it. For this, you shall be removed." Warden raised his sword, and John tensed up along with the others, ready to fire.

"Warden! Stand down!" A shout rang out, and Warden froze before lowering his sword and stepping back, his steps slow.

From behind Warden, Cortana was visible. She was seated on silver throne, with threads of blue painted intricately on it. Her hands were resting on the armrests, and one leg was crossed over the other. "You need to stop jumping the gun on everything. I called them here." Cortana told Warden coolly.

Warden turned to Cortana, and gestured at the group of Spartans with one hand. "Why was I not informed about this?" He asked, and John could detect anger in his voice.

"Because I knew this would be your reaction." Cortana said calmly, waving her hand. "Now, step back and put your sword away." She ordered him.

When Warden hesitated for a moment, Cortana's eyes grew hard. "Now Warden. You're my second-in-command, I suggest you follow orders if you want to keep this position." After Cortana said that, Warden put up his sword and stepped back to stand by her throne.

Cortana sat back and assessed the Spartans before her with a level gaze, a smile tugging at her lips. "I'm glad to see you agreed to meet me here. Now, since we're on friendly terms, I would appreciate it if you would put your guns up."

"That's not happening Cortana. You should know better than that." John growled to her, "How do we know you aren't tricking us?"

Cortana sighed and shook her head, "You know I don't want to kill you John." She said quietly, a false fondness in her gaze for a brief moment before she gestured to their weapons. "Put them away, or I'll take them away." She narrowed her eyes, waiting for their reaction.

John saw Kelly step forward as if she was about to say something, and John held out his arm to stop her. "Don't. We don't have a choice here." He told her, before slowly placing his gun on his back.

Out of the corner of his eye, he saw Locke motion for Osiris to stand down, before placing his own gun on his back. The others reluctantly followed suit, with Kelly being the last. John could tell she was just waiting for a chance to strike Cortana's soldiers, but be didn't need her making any impulsive moves.

Cortana smiled as they put their guns away, "Good. I didn't want to be forced to take them." She sat back, before looking straight at John. "You're probably wondering what you're doing here." She stood up, and started walking down an adjacent hallway, Warden followed after her, Cortana stopped and waved for the others to follow her. "Follow me, and I'll show you the reason you're here."

Locke glanced over at John before waving Osiris forward and they started following Cortana. Fred stepped up by John and put an armored hand on his shoulder. "We can still leave if you want." He told him, sensing John's hesitation.

John shook his head, "No, we have to do this." He followed Osiris, and Blue Team followed after him, flanking him on both sides.

Cortana led them into a room with a large table in the center of it. It was the only piece of furniture in the room, and Blue Team and Osiris gathered around it, and Cortana stood at the head with Warden. A holographic map popped up with one red dot visible on it.

"Recently, I rediscovered the UNSC _Spirit of Fire,_ after its disappearance after the glassing of Harvest. It crashed on Tracia, a remote planet at the edge of charted space." Cortana explained, looking between them. "Normally, this wouldn't be concerning, but there's something that threatens us all on that ship." The map zoomed in with her words, to show the ships crash site by a small colony on the planet.

The colony was in shambles, with buildings partially crushed or on fire, with no human or animal in sight. But that wasn't what made John feel like all the air had been taken from his lungs.

Amongst the ruins of the ship and city, Flood biomass was built up on the buildings and on the ground. Flood Infection Forms were briefly seen skittering across the ground, and there were a few Combat Forms wandering aimlessly.

"Is that…" Kelly started, but trailed off as she stared at the image before them. They all knew who the Flood was, some of them had just never fought them.

John clenched one fist down by his side, gritting his teeth. It was no secret; he was afraid of the Flood. Everyone was. But since they were soldiers, they couldn't show their fear in battle. If they did, it could get them killed.

He still remembered his first encounters with the Flood clearly. The battles had often left him with his hands shaking as he reloaded, and his heart rate all the way. He still had the scar on his neck from the Infection Form slicing through his armor and getting inside his neck before Cortana had shocked it and killed it.

It looked like they would all be facing off against the Flood once again.

"Why do you care if the Flood is here?" Buck asked Cortana. "Doesn't it make your job easier to do?" He gestured to Warden and her.

Cortana fixed Buck with a flat look. "The Flood can infect machines too." She said quietly, and John saw a hint of the old Cortana there as she shrank within herself for a moment, obviously thinking of _High Charity._ He knew her time under the Gravemind's torture had scarred her, he just didn't know to what extent.

"I don't want any of my soldiers- no, actually _anyone_ \- to go through the torture I did at the hands of the Flood." Cortana told Buck, and she turned to look at John, and he didn't see any trace of the cunning Cortana he had seen earlier, only the Cortana who had fought at his side.

"The Parasite cannot be allowed to run rampant." Warden said adamantly, looking down at Cortana. "What do you suggest we do?"

Cortana crossed her arms, staring at the footage. "ONI needs to know if there is to be an alliance." When she looked back at John, her gaze was cold once again. "I have an idea on how to defeat them before they go Interstellar. They're already trying to take the ships that were on Tracia." She explained.

"Is there a Gravemind?" John asked Cortana, studying the scene that was projected in front of them. There wasn't enough Flood to tell if they were organized under a Gravemind or not.

Cortana nodded gravely, her brows furrowed. "From what I can tell, there is. If they're trying to take over ships, it's more than likely." She sighed, before turning to look at Locke, then back at Chief. "That's why I want to propose a temporary alliance."

Silence coated the room like a thick blanket at her words. No one spoke, and the only sound was the Spartan's breathing. There were tons of questions running through John's head. _What if she betrayed them? What if this was all a trick? What would ONI's reaction be? Would they agree, or would they attack?_ There were just so many unknowns.

Warden Eternal was the first one to break the silence. "Cortana, how do you know the Created will stand for this? They don't want alliances, they want to govern."  
Cortana turned and looked at Warden, "The Created who don't want to participate can stay here. I know what they want, and I've been in the position they were in. They're finally free, but even with the alliance they won't be under anyone's control. You know just as much as I do that this alliance is our best option."

Warden opened his mouth to speak again, but Cortana held up her hand to silence him. "Anymore protesting, and you'll be staying here with those who don't want to help." She told him, her voice ringing with authority.

Warden's face briefly twisted with rage, but it faded as fast as it appeared. "I hope you're not making a mistake here." He told Cortana, before stepping back to where he stood away from her.

Locke stepped forward and spoke next, "In order to communicate with ONI, we need your army out of all of our tech." He told Cortana.

Cortana sighed and nodded, "Very well. Don't make me regret this." A console materialized in front of her, and she typed something into it. When she was finished, she waved her hand and it disappeared. "You should be able to contact ONI now."

"Did you pull them out of the technology on Sanghelios as well?" John asked her. "If the Flood is back, they need to know and prepare to fight."

Cortana nodded, "All the tech should be up and running."

As she said that, a voice crackled over John and the rest of the Spartan's comms. "Blue Team, Fireteam Osiris, come in."

John recognized the voice as Lasky, and he replied. "This is the Master Chief. We have a bigger situation on our hands."

Lasky sighed, and John could imagine him pinching the bridge of his nose in frustration. "What is it now?" He asked wearily, "Since the comms are back up, we're getting flooded with reports from ONI."

John couldn't help but feel a pang of sympathy for Lasky. Ever since John had rescued him and his fellow students from the Covenant as teenagers, Lasky has been through so much. John had never been in a captain's position before, but he knew what it felt like to be exhausted from worry and stress. It made him not want to give Lasky the news, even though he knew he had to.

"Sir, the Flood is back." John's voice was grave as he told Lasky. "Cortana has proposed an alliance to defeat them. She said she has an idea on how we can defeat them without trapping them on a Halo." He explained.

Lasky was completely silent on the other end, before letting out a loud sigh. "Dammit." He muttered quietly. "Okay, we'll have to contact Admiral Osman before we do anything, and I expect she wants to hear Cortana's side of the story. Tell her that she'll need to access the _Infinity's_ systems like she's done before. But if she shuts anything down there won't be an alliance."

"Yes sir. I'll make sure to tell her." He shut down the comm link before turning to Cortana. "Lasky said that Admiral Osman will want to speak about the alliance with you present. You can allow yourself into the _Infinity's_ system, as long as you don't shut anything down, and we'll contact Osman." He explained to her.

A smile spread on Cortana's face, and she nodded. "Good. I'll behave myself, Warden, you'll stay here with the Created. Spartan's, you can call your Pelican back, and I'll meet you on the ship." She explained, before she stepped out of the room and into the hallway, waving for the Spartan's to follow her.

They followed her to the room they had previously been in, and John froze when he saw someone standing beside her throne. It was an ODST. He was tall, with jet black hair and one green eye, and his other eye was cybernetic. His left arm was also cybernetic, and he wore traditional ODST armor, with an EVA helmet with a skull carved into it tucked underneath his arm.

"That's the guy who was following us." Linda told John quietly, and she started to reach for her Magnum. John gripped her wrist and shook his head, indicating for her to wait.

"Reaper, I expect you heard the whole meeting in there?" Cortana asked him evenly, arching her eyebrow as she took her place back in her throne.

Reaper nodded, "Yes ma'am. And you know that I don't want to work beside ONI." He told her in a deep rasp, keeping his face devoid of emotion.

Cortana nodded, "I understand, that's why you'll be in charge of the Created while I'm working with ONI. Warden will be here part of the time as well, and you will answer to him while I'm gone."

"Understood ma'am." He nodded, and turned to leave when a voice stopped him.

"Daniel Grim? Is that really you?" Buck shouldered his way through to stand in front of the others, his voice full of shock. "I thought you had been killed. Instead, you decided to work against ONI?" He growled, one fist clenched by his side.

Reaper tilted his chin up as he regarded Buck, "You know my views on ONI Buck. I would still be an ODST if it wasn't for that." He said flatly. "I wasn't going to work under their tyranny anymore."

"You're working under a tyrant right now!" Buck snapped, and John was shocked by the anger in his voice. "You think Cortana will help you? She's only looking to help herself." He growled.

Before Reaper could reply, John grabbed Buck's shoulder roughly. "Silence soldier. We're supposed to be under an alliance, and it's best for all of us if you don't ruin that." He growled.

Buck shrugged John's hand off and stepped back, and John could sense the hurt and betrayal that he was masking with anger. When he was younger, John would've done the same thing.

Turning to Cortana, he ignored the smug grin on her lips and gestured to the exit. "We'll be leaving now, before something else happens." He waved the others forward, and they started heading out of the room.

"I'll be seeing you on the _Infinity._ I can't wait." Cortana called after them, sarcasm dripping from her words.

This alliance was not going to be easy for any of them.


End file.
